Somatic embryogenesis in plants is a classic example of cell fate reprogramming, in which somatic cells reverse their developmental trajectory to regain totipotency, thereby serving as a valuable tool in plant biotechnology for the propagation of endangered species and the production of transgenic crops with improved traits. However, the precise cellular origins and the molecular mechanisms driving somatic cell reprogramming remain incompletely understood. A recent study revealed that the LEC2-SPCH module can synergistically activate local auxin biosynthesis, guiding stomatal-lineage precursor cells in the cotyledon epidermis to undergo cell fate transition and develop into somatic embryos. This study not only captured the entire process of a single plant somatic cell developing into a somatic embryo for the first time but also provided critical evidence for deciphering somatic reprogramming. Capitalizing on these findings, this review summarizes the regulatory mechanisms underlying cell fate reprogramming during somatic embryogenesis, with a particular focus on the synergistic interplay between auxin signaling and epigenetic reprogramming. We further discuss the potential of leveraging core reprogramming factors to enhance crop regeneration systems and outline promising future research directions.